Prof. Mark Phalen from the British Quadram Institute came up with a solution to the problem, using a new and computerized approach to combine a small group of Latin and Greek roots to create over a million new names for bacterial species, which are "on the shelf", ready to be used at any given moment by the scientists
Bacteria have settled on the Earth's surface over the years in various environments, from the upper atmosphere to the deep soil. Estimates vary regarding the number of bacterial species that exist today on our planet - from millions to billions, and the best researchers disagree about the exact number, if it can even be reached. Only in our intestines there are estimated to be thousands of species of bacteria, compare in your mind how many species exist in the entire human body. In the 18th century, the Swedish researcher Linnaeus tried to create a list of names of living creatures, which included a two-word Latin name for each species. This is how, for example, the scientific names developed for man - Homo sapiens, for lion - Felis leo, and for fig - Ficus carica. The name Escherichia coli, often shortened to E. coli, was created in a similar way by the bacteriologist Dr. Aldo Castellani and the medical researcher Dr. Albert John Chalmers, and refers to the group of bacteria essential to the functioning of the human digestive system.
Efforts to codify the names of bacteria culminated in the creation of the international nomenclature code for prokaryotes, called ICNP, which sets the rules for naming species of bacteria or species of archaea (Archaea, "primitive bacteria"). Linnaeus' lasting legacy in microbiology is evident in the ICNP's remarkable success in overseeing the publication of the names of over 3,400 genera of bacteria and archaea, and over 20,000 species of bacteria and archaea. These names are well documented in the list of prokaryotic names on the site https://www.bacterio.net.
Colonies of bacteria
Recently there has been a shortage of new names due to an increasing number of new species that have been discovered, which cannot be assigned to existing nomenclature groups. The researchers noted in their article many difficulties on the way to creating new names for bacteria. The current situation creates a lot of work for researchers and especially difficulties because almost none of the bacteriologists have enough knowledge of classical languages such as Latin and Greek to propose new names that meet the formal requirements and accepted rules. Even the greatest experts in the field of microbial naming had difficulty coming up with new names at the speed required to cope with the volume of discoveries. Moreover, bacteriologists are bound by the ICNP guidelines, which include strict rules and detailed recommendations on how new names should be formulated. These exacting requirements mean that new names must undergo linguistic quality control a long time before they are approved, through a dwindling pool of experts who are required to know classical languages and contemporary microbiology. In addition, "despite the publication of several manuals for implementation, the skill gaps between researchers resulted in the spread of serious errors - a prominent example of this appeared in the name Campylobacter pyloridis', which was verified in the International Journal of Systematic Bacteriology before it had to be corrected according to the rules of the Latin grammar for Campylobacter pylori", explained in the scientific article.
Prof. Mark Pallen from the British 'Quadram' Institute came up with a solution to the problem, using a new and computerized approach to combine a small group of Latin and Greek roots to create over a million new names for bacterial species, which are "on the shelf", ready to be used at any given moment by the scientists. Armed with the Python programming language, Prof. Palen and his partners created the computer program "Great Automatic Nomenclator" (or GAN for short), which is able to receive tables of word parts in a certain format and output according to precise scientific rules. The names created in this process were carefully checked by an expert in the nomenclature of bacterial species, Prof. Aharon Oren from the Institute of Life Sciences at the Hebrew University of Jerusalem, while the bioinformatician Dr. Andrea Taltin, also from the Quadram Institute, wrote a computer program to automate the process. The researchers examined combinations of prefixes and suffixes, names of unique places and names of famous scientists from the past, or a description of the habitat or biome in which the bacterium lived ("In the age of metagenomics and extensive research of the microbiome, we need names for new species for hundreds of 'inhabitants' of the microbiome" ).
The next million names for bacteria
Not for nothing is the title of the study "The Next Million Names for Archaea and Bacteria". The researchers noted that "we have shown how the combinatorial use of Greek and Latin roots can be used to create more than a million new and creative names for bacteria new to science. To the best of our knowledge, the move we made is actually the greatest creation in the history of science of names that can be given to bacteria."
"Microbiology has recently entered a golden period of new discoveries, with exponential growth in the identification of new species following the development of various genomic and meta-genomic methods. This situation creates an urgent and unmet need to establish new taxonomic names for bacteria.. Should we be satisfied if a new species named UBA6965 or sp000063525 is created? We believe the answer should be 'No!' Resonant.. We argue that the problem can best be solved by automating the generation of new and designed names.. To meet the obvious need to create nomenclature for a million new bacteria or archaeon species, we propose to abandon the current approach and instead aim for the automated and mass generation of New names, for the purpose of assigning them to different biological bodies. Is this even possible? An answer to this can be found if we go back to the classical times to create root combinations of individual words from Greek or Latin that will contribute to the development of complex words with meanings.. We believe that our approach serves as a sort of road map for anyone who wants to create new names in the coming decades," the scientific article states.
The researchers' work was recently published in the journal "Trends in Microbiology". Prof. Palen, Prof. Oren and Dr. Teltin created a digital warehouse of grammatically correct names, which can be used in scientific articles according to the needs of their fellow bacteriologists. The list they created includes names for bacteria associated with certain animals or certain living systems - for example, a name like Equimonas can be applied to a new bacterium isolated from horses, and the name Intestinimicrobium can be applied to a new bacterium isolated from the intestine. They also included a set of names honoring famous scientists who passed away or names from Greek mythology, such as Charles Darwin, Willie Hennig, or names from Greek mythology such as Calypso - to create names for new genera such as "Darwiniimicrobium", "Darwiniimonas", or "Calypsomicrobium". "We compiled a balanced, multi-gender list of 80 worthy scientists and used our software to generate 640 new names from this list, including Darwiniibacterium and Hennigiimonas," the scientific paper reads.
"It's amazing to me to see that our software, 'Great Automatic Nomenclator', is joining the global big data world. Version 1.0 still requires detailed collection of the input files and produces fairly basic outputs that can be finished by editing in Excel. However, we anticipate that the program will become more user-friendly and productive in the following versions," said Prof. Oren and Dr. Telatin added: "For me, this is just the beginning of the process. We predict that one day, naming bacteria will be as easy a process as performing a Google search. Happily, our computer software is available for use by anyone who wishes to use it."
For further reading, a scientific article is attached
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